One guys of my team reports that we have duplicate alerts for HA and DRS, so I took a look close and here the alerts :

So each of my collectors servers generated this alert, but if we look in the configuration, CENCluster01 must be only monitored by BRAMOMVSP001, so why the two others collectors servers also generated this alerts ?

I found exactly the same stuff for a RDS alert :
bramomvsp001: CRITICAL:Error:XXX-XXX\BRAMOMVSP001:nworks vCenter: DRS invocation failed in Cluster:SCOM :nworks.VMware.VEM.VIAPILink:BRAMOMVSP001.xxx.xxx-xxx.com;bravmvcap001.xxx.xxx-xxx.com: DRS invocation not completedDrsInvocationFailedEvent:8/12/2010 10:59:14 PM:BraCluster03:XXX

The HA, VMotion, DRS.....are the alerts, that are processed by nworks based on the VCenter events.
By default, all your Collectors are connected to VC and set to process these events, though you have overall load balanced and each collector has it's own cluster...hosts to monitor, that is the reason you get duplicated alerts.
You can easy fix this in Nworks Enterprise Manager: Go to ....SP002 and ....SP003 Collectors one after another, and modify the Advanced Settings, find
"EnableVcGenericEvents" parameter and make "False". Leave this parameter by default on your ....SP001 collector.
This is the way you won't get duplicated alerts any more.
But please note, that if ...SP001 collector goes down and failover occurs to another collectors where we have it disabled, it won't turn on these events automatically in current version of nworks.

Are they plans to fix this (singular alerts with multiple collectors and having failover capability) ? or is there a way in the meantime of programatically enabling\disabling the EnableVcGenericEvents setting ?

The automated assignment and failover of the 'generic VC events' setting is already in development for the next nworks update

Meanwhile there is no programmatic way out-of-box in nworks to set the EnableVcGenericEvents setting; however it is simply a registry key setting as follows:
HKEY_LOCAL_MACHINE\SOFTWARE\nworks\VIC\Collector\GlobalSettings
DWORD Name: EnableVcGenericEvents
Values: 0 (False), 1 (True, default)
Default is used if the key is not present.
You can set/create the registry key using a script or other method.